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vidjil
vidjil
Commits
880abf7d
Commit
880abf7d
authored
Sep 13, 2017
by
Mathieu Giraud
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should-get-tests/*.should-get: replace $VIDJIL_DIR/data by $VIDJIL_DATA
See
#2611
.
parent
35525c10
Changes
70
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70 changed files
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72 additions
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72 deletions
+72
-72
algo/tests/should-get-tests/10-md5-data.should-get
algo/tests/should-get-tests/10-md5-data.should-get
+1
-1
algo/tests/should-get-tests/ambiguous_representative.should-get
...ests/should-get-tests/ambiguous_representative.should-get
+1
-1
algo/tests/should-get-tests/ambiguous_representative2.should-get
...sts/should-get-tests/ambiguous_representative2.should-get
+1
-1
algo/tests/should-get-tests/cdr3-stopcodon.should-get
algo/tests/should-get-tests/cdr3-stopcodon.should-get
+1
-1
algo/tests/should-get-tests/cgi-align.should-get
algo/tests/should-get-tests/cgi-align.should-get
+1
-1
algo/tests/should-get-tests/cgi-align2.should-get
algo/tests/should-get-tests/cgi-align2.should-get
+1
-1
algo/tests/should-get-tests/cgi-align3.should-get
algo/tests/should-get-tests/cgi-align3.should-get
+1
-1
algo/tests/should-get-tests/chimera-fake-2.should-get
algo/tests/should-get-tests/chimera-fake-2.should-get
+1
-1
algo/tests/should-get-tests/chimera-fake-D.should-get
algo/tests/should-get-tests/chimera-fake-D.should-get
+1
-1
algo/tests/should-get-tests/chimera-fake-VJ-germlines-trim.should-get
...hould-get-tests/chimera-fake-VJ-germlines-trim.should-get
+1
-1
algo/tests/should-get-tests/chimera-fake-VJ-germlines.should-get
...sts/should-get-tests/chimera-fake-VJ-germlines.should-get
+1
-1
algo/tests/should-get-tests/chimera-fake-VJ.should-get
algo/tests/should-get-tests/chimera-fake-VJ.should-get
+1
-1
algo/tests/should-get-tests/chimera-fake-half.should-get
algo/tests/should-get-tests/chimera-fake-half.should-get
+1
-1
algo/tests/should-get-tests/chimera-fake.should-get
algo/tests/should-get-tests/chimera-fake.should-get
+1
-1
algo/tests/should-get-tests/chimera.should-get
algo/tests/should-get-tests/chimera.should-get
+1
-1
algo/tests/should-get-tests/clones_lec.should-get
algo/tests/should-get-tests/clones_lec.should-get
+1
-1
algo/tests/should-get-tests/clones_simul.should-get
algo/tests/should-get-tests/clones_simul.should-get
+1
-1
algo/tests/should-get-tests/clones_simul_cluster.should-get
algo/tests/should-get-tests/clones_simul_cluster.should-get
+1
-1
algo/tests/should-get-tests/common-V-D.should-get
algo/tests/should-get-tests/common-V-D.should-get
+1
-1
algo/tests/should-get-tests/example_mouse.should-get
algo/tests/should-get-tests/example_mouse.should-get
+1
-1
algo/tests/should-get-tests/gzip.should-get
algo/tests/should-get-tests/gzip.should-get
+1
-1
algo/tests/should-get-tests/large-N.should-get
algo/tests/should-get-tests/large-N.should-get
+1
-1
algo/tests/should-get-tests/multi-complete.should-get
algo/tests/should-get-tests/multi-complete.should-get
+1
-1
algo/tests/should-get-tests/multi-i-complete.should-get
algo/tests/should-get-tests/multi-i-complete.should-get
+1
-1
algo/tests/should-get-tests/multi-i-short.should-get
algo/tests/should-get-tests/multi-i-short.should-get
+1
-1
algo/tests/should-get-tests/multi-segment.should-get
algo/tests/should-get-tests/multi-segment.should-get
+1
-1
algo/tests/should-get-tests/multi-short-affects.should-get
algo/tests/should-get-tests/multi-short-affects.should-get
+1
-1
algo/tests/should-get-tests/multi-short.should-get
algo/tests/should-get-tests/multi-short.should-get
+1
-1
algo/tests/should-get-tests/multi-tiny-segment.should-get
algo/tests/should-get-tests/multi-tiny-segment.should-get
+1
-1
algo/tests/should-get-tests/overlap-stdout.should-get
algo/tests/should-get-tests/overlap-stdout.should-get
+1
-1
algo/tests/should-get-tests/quality-json.should-get
algo/tests/should-get-tests/quality-json.should-get
+1
-1
algo/tests/should-get-tests/revcomp.should-get
algo/tests/should-get-tests/revcomp.should-get
+1
-1
algo/tests/should-get-tests/segment_S22.should-get
algo/tests/should-get-tests/segment_S22.should-get
+1
-1
algo/tests/should-get-tests/segment_simul.should-get
algo/tests/should-get-tests/segment_simul.should-get
+1
-1
algo/tests/should-get-tests/segmentation-D-read-number.should-get
...ts/should-get-tests/segmentation-D-read-number.should-get
+3
-3
algo/tests/should-get-tests/sequences_of_interest.should-get
algo/tests/should-get-tests/sequences_of_interest.should-get
+1
-1
algo/tests/should-get-tests/several-g.should-get
algo/tests/should-get-tests/several-g.should-get
+1
-1
algo/tests/should-get-tests/stanford-X100-sampled.should-get
algo/tests/should-get-tests/stanford-X100-sampled.should-get
+1
-1
algo/tests/should-get-tests/stanford-debug.should-get
algo/tests/should-get-tests/stanford-debug.should-get
+1
-1
algo/tests/should-get-tests/stanford-detailed.should-get
algo/tests/should-get-tests/stanford-detailed.should-get
+1
-1
algo/tests/should-get-tests/stanford-fuse.should-get
algo/tests/should-get-tests/stanford-fuse.should-get
+1
-1
algo/tests/should-get-tests/stanford-json.should-get
algo/tests/should-get-tests/stanford-json.should-get
+1
-1
algo/tests/should-get-tests/stanford-k14.should-get
algo/tests/should-get-tests/stanford-k14.should-get
+1
-1
algo/tests/should-get-tests/stanford-labels-FaW.should-get
algo/tests/should-get-tests/stanford-labels-FaW.should-get
+1
-1
algo/tests/should-get-tests/stanford-labels-W.should-get
algo/tests/should-get-tests/stanford-labels-W.should-get
+1
-1
algo/tests/should-get-tests/stanford-labels.should-get
algo/tests/should-get-tests/stanford-labels.should-get
+1
-1
algo/tests/should-get-tests/stanford-segment-x100-first.should-get
...s/should-get-tests/stanford-segment-x100-first.should-get
+1
-1
algo/tests/should-get-tests/stanford-t1.should-get
algo/tests/should-get-tests/stanford-t1.should-get
+1
-1
algo/tests/should-get-tests/stanford-vidjil-to-fasta.should-get
...ests/should-get-tests/stanford-vidjil-to-fasta.should-get
+1
-1
algo/tests/should-get-tests/stanford-w100.should-get
algo/tests/should-get-tests/stanford-w100.should-get
+1
-1
algo/tests/should-get-tests/stanford-wall.should-get
algo/tests/should-get-tests/stanford-wall.should-get
+1
-1
algo/tests/should-get-tests/stanford-x100-first.should-get
algo/tests/should-get-tests/stanford-x100-first.should-get
+1
-1
algo/tests/should-get-tests/stanford-xyz-yall.should-get
algo/tests/should-get-tests/stanford-xyz-yall.should-get
+1
-1
algo/tests/should-get-tests/stanford-xyz.should-get
algo/tests/should-get-tests/stanford-xyz.should-get
+1
-1
algo/tests/should-get-tests/stanford.should-get
algo/tests/should-get-tests/stanford.should-get
+1
-1
algo/tests/should-get-tests/tools-align.should-get
algo/tests/should-get-tests/tools-align.should-get
+1
-1
algo/tests/should-get-tests/tools-similarity.should-get
algo/tests/should-get-tests/tools-similarity.should-get
+1
-1
algo/tests/should-get-tests/trb-only-VJ.should-get
algo/tests/should-get-tests/trb-only-VJ.should-get
+1
-1
algo/tests/should-get-tests/trd-dd2-dd3-complete.should-get
algo/tests/should-get-tests/trd-dd2-dd3-complete.should-get
+1
-1
algo/tests/should-get-tests/trd-dd2-dd3-incomplete.should-get
.../tests/should-get-tests/trd-dd2-dd3-incomplete.should-get
+1
-1
algo/tests/should-get-tests/trd-dd2-dd3.should-get
algo/tests/should-get-tests/trd-dd2-dd3.should-get
+1
-1
algo/tests/should-get-tests/unsegmentation-causes-u.should-get
...tests/should-get-tests/unsegmentation-causes-u.should-get
+1
-1
algo/tests/should-get-tests/unsegmentation-causes.should-get
algo/tests/should-get-tests/unsegmentation-causes.should-get
+1
-1
algo/tests/should-get-tests/vidjil-error-w-small.should-get
algo/tests/should-get-tests/vidjil-error-w-small.should-get
+1
-1
algo/tests/should-get-tests/vidjil-small-w.should-get
algo/tests/should-get-tests/vidjil-small-w.should-get
+1
-1
algo/tests/should-get-tests/vidjil-warning-A.should-get
algo/tests/should-get-tests/vidjil-warning-A.should-get
+1
-1
algo/tests/should-get-tests/vidjil-warning-z.should-get
algo/tests/should-get-tests/vidjil-warning-z.should-get
+1
-1
algo/tests/should-get-tests/vidjil_long_segment.should-get
algo/tests/should-get-tests/vidjil_long_segment.should-get
+1
-1
algo/tests/should-get-tests/vidjil_revcomp_VdJa.should-get
algo/tests/should-get-tests/vidjil_revcomp_VdJa.should-get
+1
-1
algo/tests/should-get-tests/vidjil_revcomp_s22.should-get
algo/tests/should-get-tests/vidjil_revcomp_s22.should-get
+1
-1
No files found.
algo/tests/should-get-tests/10-md5-data.should-get
View file @
880abf7d
!NO_LAUNCHER:
!LAUNCH: (cd $VIDJIL_D
IR/data
; md5sum *.fasta || md5 -r *.fasta)
!LAUNCH: (cd $VIDJIL_D
ATA
; md5sum *.fasta || md5 -r *.fasta)
$ Check md5 in data/
1:985219d9156b6d9e8966807595beada3 Stanford_S22.fa
...
...
algo/tests/should-get-tests/ambiguous_representative.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -k 4 -w 20 -z 0 -c clones -V $VIDJIL_D
IR/data/toy_V.fa -J $VIDJIL_DIR/data/toy_J.fa $VIDJIL_DIR/data
/ambiguous_representative.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -k 4 -w 20 -z 0 -c clones -V $VIDJIL_D
ATA/toy_V.fa -J $VIDJIL_DATA/toy_J.fa $VIDJIL_DATA
/ambiguous_representative.fa
$ Short reads properly segmented
1:SEG_+.* -> .* 4
...
...
algo/tests/should-get-tests/ambiguous_representative2.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -c clones -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/test_representatives.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -c clones -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/test_representatives.fa
$ Three clones should be found
1:3 clones
...
...
algo/tests/should-get-tests/cdr3-stopcodon.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_D
IR/data
/cdr3-stopcodon.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_D
ATA
/cdr3-stopcodon.fa
!LOG: out/cdr3-stopcodon.vidjil
$ Two identical junctions in JSON
...
...
algo/tests/should-get-tests/cgi-align.should-get
View file @
880abf7d
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_D
IR/data
/msa.fa
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_D
ATA
/msa.fa
$ no spurious info
0: .* bp in .* sequences
...
...
algo/tests/should-get-tests/cgi-align2.should-get
View file @
880abf7d
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_D
IR/data
/msa2.fa
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_D
ATA
/msa2.fa
$ no spurious info
0: .* bp in .* sequences
...
...
algo/tests/should-get-tests/cgi-align3.should-get
View file @
880abf7d
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_D
IR/data
/msa3.fa
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_D
ATA
/msa3.fa
$ no spurious info
0: .* bp in .* sequences
...
...
algo/tests/should-get-tests/chimera-fake-2.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -t 0 -g $VIDJIL_DIR/germline -2 $VIDJIL_D
IR/data
/chimera-fake.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -t 0 -g $VIDJIL_DIR/germline -2 $VIDJIL_D
ATA
/chimera-fake.fa
$ The KmerSegmenter segments the three chimera reads on PSEUDO_MAX12 germline (-2)
1:unexpected .* -> .* 3
...
...
algo/tests/should-get-tests/chimera-fake-D.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_D
IR/data
/chimera-fake-D.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_D
ATA
/chimera-fake-D.fa
$ The KmerSegmenter segments the chimera reads on PSEUDO_MAX12 germline (-2)
f1:unexpected .* -> .* 2
...
...
algo/tests/should-get-tests/chimera-fake-VJ-germlines-trim.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_D
IR/data/chimera-fake-VJ-trim.g $VIDJIL_DIR/data
/chimera-fake-VJ.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_D
ATA/chimera-fake-VJ-trim.g $VIDJIL_DATA
/chimera-fake-VJ.fa
# Testing a custom (fake) .g with special parameters for the algorithm
$ The KmerSegmenter segments no read in Y because of the parameter
...
...
algo/tests/should-get-tests/chimera-fake-VJ-germlines.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_D
IR/data/chimera-fake-VJ.g $VIDJIL_DIR/data
/chimera-fake-VJ.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_D
ATA/chimera-fake-VJ.g $VIDJIL_DATA
/chimera-fake-VJ.fa
# Testing a custom (fake) germlines.data
$ Report the species
...
...
algo/tests/should-get-tests/chimera-fake-VJ.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_D
IR/data
/chimera-fake-VJ.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_D
ATA
/chimera-fake-VJ.fa
$ The KmerSegmenter segments the five chimera reads on PSEUDO_MAX12 germline (-2)
1:unexpected .* -> .* 5
...
...
algo/tests/should-get-tests/chimera-fake-half.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 100 -A -t 0 -g $VIDJIL_DIR/germline -4 $VIDJIL_D
IR/data
/chimera-fake-half.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 100 -A -t 0 -g $VIDJIL_DIR/germline -4 $VIDJIL_D
ATA
/chimera-fake-half.fa
# TODO: a more precise modeling should give a e-value computation that could make this work even with -e 1
$ The KmerSegmenter segments the six chimera reads on PSEUDO_MAX1U germline (-4)
...
...
algo/tests/should-get-tests/chimera-fake.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_D
IR/data
/chimera-fake.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_D
ATA
/chimera-fake.fa
$ Do not segment on any germline, even incomplete
1:junction detected in 0 reads
...
...
algo/tests/should-get-tests/chimera.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -uU -g $VIDJIL_DIR/germline $VIDJIL_D
IR/data
/chimera-trg.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -uU -g $VIDJIL_DIR/germline $VIDJIL_D
ATA
/chimera-trg.fa
$ Do not segment on IGL by chance
f1:IGL .* -> .* 0
...
...
algo/tests/should-get-tests/clones_lec.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -c clones -A -3 $VIDJIL_D
IR/data
/segment_lec.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -c clones -A -3 $VIDJIL_D
ATA
/segment_lec.fa
$ Extract 50bp windows (TRG)
1:found . 50-windows
...
...
algo/tests/should-get-tests/clones_simul.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 1 -r 1 $VIDJIL_D
IR/data
/clones_simul.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 1 -r 1 $VIDJIL_D
ATA
/clones_simul.fa
$ Junction extractions
1:found 25 50-windows in 66 reads
...
...
algo/tests/should-get-tests/clones_simul_cluster.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 0 -r 1 -n 5 $VIDJIL_D
IR/data
/clones_simul.fa ; cat out/clones_simul.vidjil
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 0 -r 1 -n 5 $VIDJIL_D
ATA
/clones_simul.fa ; cat out/clones_simul.vidjil
$ Window extractions
2:found 25 50-windows in 66 reads
...
...
algo/tests/should-get-tests/common-V-D.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -KA -z 0 -s \\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\# -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa $VIDJIL_D
IR/data
/common-V-D.fa ; cat out/common-V-D.affects
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -KA -z 0 -s \\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\# -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa $VIDJIL_D
ATA
/common-V-D.fa ; cat out/common-V-D.affects
$ Segments the sequence
1: SEG .* -> .* 1
...
...
algo/tests/should-get-tests/example_mouse.should-get
View file @
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!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -c segment -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_D
IR/data
/example_mouse.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -c segment -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_D
ATA
/example_mouse.fa
$ Segment sequence on IGK
1:segIGK.*IGKV.*IGKJ
...
...
algo/tests/should-get-tests/gzip.should-get
View file @
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!NO_LAUNCHER:
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data/clones_simul.fa > out-fa ; $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -b clones_simul $VIDJIL_DIR/data
/clones_simul.fa.gz > out-fa-gz ; diff -s -I '\#' -I 'index' -I 'data/clones_simul' out-fa out-fa-gz ; echo 'Diff: '\\$?; wc -l out-fa-gz
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA/clones_simul.fa > out-fa ; $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -b clones_simul $VIDJIL_DATA
/clones_simul.fa.gz > out-fa-gz ; diff -s -I '\#' -I 'index' -I 'data/clones_simul' out-fa out-fa-gz ; echo 'Diff: '\\$?; wc -l out-fa-gz
$ Identical output
1:Diff: 0
...
...
algo/tests/should-get-tests/large-N.should-get
View file @
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!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -r 1 $VIDJIL_D
IR/data
/large_N.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -r 1 $VIDJIL_D
ATA
/large_N.fa
$ Find a huge insertion in the segmentation
1:>clone-001.*/[ACGT]{100}
algo/tests/should-get-tests/multi-complete.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_D
IR/data
/multi-complete.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_D
ATA
/multi-complete.fa
$ Segment all the seven reads
1:junction detected in 7 reads
...
...
algo/tests/should-get-tests/multi-i-complete.should-get
View file @
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!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_D
IR/data
/multi-complete.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_D
ATA
/multi-complete.fa
$ Segment all the seven reads
1:junction detected in 7 reads
...
...
algo/tests/should-get-tests/multi-i-short.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_D
IR/data
/multi-short.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_D
ATA
/multi-short.fa
$ Segment all the seven reads
1:junction detected in 7 reads
...
...
algo/tests/should-get-tests/multi-segment.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil -c segment $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH,IGK,IGL $VIDJIL_D
IR/data
/multi-complete.fa ; cat out/multi-complete.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
!LAUNCH: $VIDJIL_DIR/vidjil -c segment $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH,IGK,IGL $VIDJIL_D
ATA
/multi-complete.fa ; cat out/multi-complete.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
$ Segment the Ig recombinations
1:IGH SEG
...
...
algo/tests/should-get-tests/multi-short-affects.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 5 -K -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL $VIDJIL_D
IR/data
/multi-short.fa ; head -n 17 out/multi-short.affects
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 5 -K -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL $VIDJIL_D
ATA
/multi-short.fa ; head -n 17 out/multi-short.affects
# Testing .affects output (-K)
$ First sequence (TRA), display sequence
...
...
algo/tests/should-get-tests/multi-short.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRG,TRD,IGH,IGK,IGL $VIDJIL_D
IR/data
/multi-short.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRG,TRD,IGH,IGK,IGL $VIDJIL_D
ATA
/multi-short.fa
$ Segment all the seven reads
1:junction detected in 7 reads
...
...
algo/tests/should-get-tests/multi-tiny-segment.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -g $VIDJIL_DIR/germline $VIDJIL_D
IR/data
/multi-tiny.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -g $VIDJIL_DIR/germline $VIDJIL_D
ATA
/multi-tiny.fa
$ Do not segment any of the seven reads
7:UNSEG
...
...
algo/tests/should-get-tests/overlap-stdout.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -A $VIDJIL_D
IR/data
/overlap-d-j.fa | grep -v web | tail -4 | tr -d '\\\\n' | wc -c
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -A $VIDJIL_D
ATA
/overlap-d-j.fa | grep -v web | tail -4 | tr -d '\\\\n' | wc -c
$ Exported sequence has all the bases
1:116
...
...
algo/tests/should-get-tests/quality-json.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c clones -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -A $VIDJIL_D
IR/data
/segment_lec.fq > /dev/null ; cat out/segment_lec.vidjil
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c clones -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -A $VIDJIL_D
ATA
/segment_lec.fq > /dev/null ; cat out/segment_lec.vidjil
$ Window
1:"id": "GGGGTCTATTACTGTGCCACCTGGGCCTTATTATAAGAAACTCTTTGGCA"
...
...
algo/tests/should-get-tests/revcomp.should-get
View file @
880abf7d
!LAUNCH: $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 9 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -K -c clones $VIDJIL_D
IR/data
/revcomp.fa ; grep 'X.X.X' out/revcomp.affects | sed 's/[^X]//g' | sort -u ; grep '#>' out/revcomp.affects | sed 's/.*SEG.../e-value:/' | cut -f 1 -d' '
!LAUNCH: $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 9 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -K -c clones $VIDJIL_D
ATA
/revcomp.fa ; grep 'X.X.X' out/revcomp.affects | sed 's/[^X]//g' | sort -u ; grep '#>' out/revcomp.affects | sed 's/.*SEG.../e-value:/' | cut -f 1 -d' '
$ Segments both reads, normal and reverse
1:junction detected in 2 reads
...
...
algo/tests/should-get-tests/segment_S22.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -c segment $VIDJIL_D
IR/data
/segment_S22.fa | grep '^>' ; cat out/segment_S22.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -c segment $VIDJIL_D
ATA
/segment_S22.fa | grep '^>' ; cat out/segment_S22.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
$ First sequence Stanford
# 164 175 195 203
...
...
algo/tests/should-get-tests/segment_simul.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -v -g $VIDJIL_DIR/germline -c segment $VIDJIL_D
IR/data
/segment_simul.fa | grep '^[>#]'
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -v -g $VIDJIL_DIR/germline -c segment $VIDJIL_D
ATA
/segment_simul.fa | grep '^[>#]'
$ First sequence, easy segmentation (no error, few deletions at the windows, small N)
...
...
algo/tests/should-get-tests/segmentation-D-read-number.should-get
View file @
880abf7d
...
...
@@ -6,9 +6,9 @@
# other reads. This is what is tested, we first put 10 sequences, then 5 and
# finally just the sequence of interest alone.
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/buggy-D.fa; \
$VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -x 6 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/buggy-D.fa;\
$VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -x 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/buggy-D.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/buggy-D.fa; \
$VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -x 6 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/buggy-D.fa;\
$VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -x 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/buggy-D.fa
$ Three times the same window
3: TGTGCGGGATCTTCGTCCTCTTATCATAATAATGGTTTTTTGGCGGGGGAGTCATGGGGC
...
...
algo/tests/should-get-tests/sequences_of_interest.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -W ACCGGTATTACT -W CAGCTGCTCCCC -W TGGGCCACTC -W ATCAACGCTGGCAATGGTAACACTAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATACGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTCTGTATTACTGTGCGAGAGTGCGCAGCAGCTGGTCTGATGCTTTTGATTATCTGG $VIDJIL_D
IR/data
/clones_simul.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -W ACCGGTATTACT -W CAGCTGCTCCCC -W TGGGCCACTC -W ATCAACGCTGGCAATGGTAACACTAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATACGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTCTGTATTACTGTGCGAGAGTGCGCAGCAGCTGGTCTGATGCTTTTGATTATCTGG $VIDJIL_D
ATA
/clones_simul.fa
$ ACCGGTATTACT is found (in window and representative and in the command line)
3:ACCGGTATTACT
...
...
algo/tests/should-get-tests/several-g.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline -g $VIDJIL_DIR/germline/homo-sapiens-isotypes.g $VIDJIL_D
IR/data
/isotypes.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline -g $VIDJIL_DIR/germline/homo-sapiens-isotypes.g $VIDJIL_D
ATA
/isotypes.fa
$ Report the correct species
1: Homo sapiens .9606.
...
...
algo/tests/should-get-tests/stanford-X100-sampled.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -X 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/Stanford_S22.fasta
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -X 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/Stanford_S22.fasta
$ Skip the good number of reads
1:Processing every 131th read
...
...
algo/tests/should-get-tests/stanford-debug.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -\# FA -k 16 -z 0 -w 60 -r 5 -o out2 -uuu -U -v -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa $VIDJIL_D
IR/data
/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep UNSEG out2/Stanford_S22.unsegmented.vdj.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -\# FA -k 16 -z 0 -w 60 -r 5 -o out2 -uuu -U -v -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa $VIDJIL_D
ATA
/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep UNSEG out2/Stanford_S22.unsegmented.vdj.fa
# Testing uncommon and debug options
$ verbose (-v)
...
...
algo/tests/should-get-tests/stanford-detailed.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 2 -r 5 -a -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/Stanford_S22.fasta ; cat out/seq/clone.fa-2
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 2 -r 5 -a -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/Stanford_S22.fasta ; cat out/seq/clone.fa-2
# Testing detailed clone output (-a)
$ Detailed clone output (out/seq/clone.fa-2), germline
...
...
algo/tests/should-get-tests/stanford-fuse.should-get
View file @
880abf7d
!REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 0 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/fuse.py out/Stanford_S22.vidjil out/Stanford_S22.vidjil -o out/fused.data ; cat out/fused.data | python $VIDJIL_DIR/tools/format_json.py -1
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 0 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/fuse.py out/Stanford_S22.vidjil out/Stanford_S22.vidjil -o out/fused.data ; cat out/fused.data | python $VIDJIL_DIR/tools/format_json.py -1
$ Points list
e1:"original_names": ["../../..//data/Stanford_S22.fasta", "../../..//data/Stanford_S22.fasta"]
...
...
algo/tests/should-get-tests/stanford-json.should-get
View file @
880abf7d
!REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -w 60 -r 5 -e 10 -b data $VIDJIL_D
IR/data
/Stanford_S22.fasta > /dev/null ; cat out/data.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -w 60 -r 5 -e 10 -b data $VIDJIL_D
ATA
/Stanford_S22.fasta > /dev/null ; cat out/data.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
$ From homo-sapiens.g
1:"ref": "http://www.vidjil.org/germlines/germline-.*.tar.gz"
...
...
algo/tests/should-get-tests/stanford-k14.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -k 14 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/Stanford_S22.fasta
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -k 14 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/Stanford_S22.fasta
!LOG: stanford-k14.log
$ Find the good number of windows in Stanford S22 (contiguous seed 14)
...
...
algo/tests/should-get-tests/stanford-labels-FaW.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 2000 -t 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -FaW GAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACT $VIDJIL_D
IR/data
/Stanford_S22.fasta ; cat out/seq/clone.fa-1
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 2000 -t 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -FaW GAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACT $VIDJIL_D
ATA
/Stanford_S22.fasta ; cat out/seq/clone.fa-1
$ Keep only one windows, the one given by -W, with only 2 reads in the first 2000 reads (it is actually the second clone in Stanford_S22.fasta)
1: keep 1 windows in 2 reads
...
...
algo/tests/should-get-tests/stanford-labels-W.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 100 -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -r 5 -W ACTGTGCGAGAGTTGGAATTAGTAGTGGCTGGCCTGATTCCTGGGGCCAG $VIDJIL_D
IR/data
/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 100 -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -r 5 -W ACTGTGCGAGAGTTGGAATTAGTAGTGGCTGGCCTGATTCCTGGGGCCAG $VIDJIL_D
ATA
/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil
$ Some clone has only one read, bypassing the -r 5 option, and the good label
1: clone-00..*0001-.* -W
...
...
algo/tests/should-get-tests/stanford-labels.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -x 100 -r 5 -l $VIDJIL_D
IR/data/Stanford_S22.label $VIDJIL_DIR/data
/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -x 100 -r 5 -l $VIDJIL_D
ATA/Stanford_S22.label $VIDJIL_DATA
/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil
$ Some clone has only one read, bypassing the -r 5 option, and the good label
1: clone-00..*0001-.* my-clone
...
...
algo/tests/should-get-tests/stanford-segment-x100-first.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -x 2 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/Stanford_S22.fasta
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -x 2 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/Stanford_S22.fasta
$ Segments the good number of sequences in Stanford S22
2: >lcl
...
...
algo/tests/should-get-tests/stanford-t1.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -t 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -x 100 $VIDJIL_D
IR/data
/Stanford_S22.fasta
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -t 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -x 100 $VIDJIL_D
ATA
/Stanford_S22.fasta
$ No read segmented as we have no germline because of the -t
1: UNSEG too few V/J -> 100
algo/tests/should-get-tests/stanford-vidjil-to-fasta.should-get
View file @
880abf7d
!REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 100 -r 1 -z 5 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/vidjil-to-fasta.py -o out/S22.fasta out/Stanford_S22.vidjil ;
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 100 -r 1 -z 5 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/vidjil-to-fasta.py -o out/S22.fasta out/Stanford_S22.vidjil ;
!OUTPUT_FILE: out/S22.fasta
$ 5 representative sequences in the FASTA output file
...
...
algo/tests/should-get-tests/stanford-w100.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -y 0 -s '#####-#####' -w 100 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa $VIDJIL_D
IR/data
/Stanford_S22.fasta
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -y 0 -s '#####-#####' -w 100 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa $VIDJIL_D
ATA
/Stanford_S22.fasta
!LOG: stanford-w100.log
$ Find the good number of "too short sequences" for windows of size 100
...
...
algo/tests/should-get-tests/stanford-wall.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -w all -r 1 -y 15 -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/Stanford_S22.fasta
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -w all -r 1 -y 15 -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/Stanford_S22.fasta
# Testing '-w all' option
...
...
algo/tests/should-get-tests/stanford-x100-first.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -x 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/Stanford_S22.fasta
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -x 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/Stanford_S22.fasta
$ Analyze the good number of sequences in Stanford S22
1: found .* of 100 reads
algo/tests/should-get-tests/stanford-xyz-yall.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -x 10 -y all -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -x 10 -y all -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa
# Testing -x/-y/-z options
...
...
algo/tests/should-get-tests/stanford-xyz.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -x 10 -y 5 -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -x 10 -y 5 -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa
# Testing -x/-y/-z options
...
...
algo/tests/should-get-tests/stanford.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -z 0 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -s \\\\#\\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\#\\\\# $VIDJIL_D
IR/data
/Stanford_S22.fasta
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -z 0 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -s \\\\#\\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\#\\\\# $VIDJIL_D
ATA
/Stanford_S22.fasta
$ Germlines are custom
1: custom germlines
...
...
algo/tests/should-get-tests/tools-align.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/algo/tools/align -m 6 -i 0 -j 1 $VIDJIL_D
IR/data
/msa.fa
!LAUNCH: $VIDJIL_DIR/algo/tools/align -m 6 -i 0 -j 1 $VIDJIL_D
ATA
/msa.fa
$ Default cost and parameters
1: (4, -6/-10/-10, -9999-9999/-9999-9999, -1, -2)
...
...
algo/tests/should-get-tests/tools-similarity.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/algo/tools/similarity $VIDJIL_D
IR/data
/msa.fa
!LAUNCH: $VIDJIL_DIR/algo/tools/similarity $VIDJIL_D
ATA
/msa.fa
$ Read 3 sequences
1: 54 bp in .* 3 sequences
...
...
algo/tests/should-get-tests/trb-only-VJ.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRB $VIDJIL_D
IR/data
/trb-only-VJ.fa ; cat out/trb-only-VJ.vidjil
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRB $VIDJIL_D
ATA
/trb-only-VJ.fa ; cat out/trb-only-VJ.vidjil
$ Segments the read on TRB (the information is given twice, stdout + .vidjil)
2: TRB .* -> .* 1
...
...
algo/tests/should-get-tests/trd-dd2-dd3-complete.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRD $VIDJIL_D
IR/data
/trd-dd2-dd3.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRD $VIDJIL_D
ATA
/trd-dd2-dd3.fa
$ Segment only 2 reads, because we do not look for incomplete recombinations
1:junction detected in 2 reads
...
...
algo/tests/should-get-tests/trd-dd2-dd3-incomplete.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -w 10 -e 10 -A -g $VIDJIL_DIR/germline $VIDJIL_D
IR/data
/trd-dd2-dd3.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -w 10 -e 10 -A -g $VIDJIL_DIR/germline $VIDJIL_D
ATA
/trd-dd2-dd3.fa
$ Segment 5 reads, thanks to -i
1:junction detected in 5 reads
...
...
algo/tests/should-get-tests/trd-dd2-dd3.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -k 8 -w 20 -V $VIDJIL_DIR/germline/homo-sapiens/TRDV.fa -V $VIDJIL_DIR/germline/homo-sapiens/TRDD2_upstream.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDD3_downstream.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDJ.fa $VIDJIL_D
IR/data
/trd-dd2-dd3.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -k 8 -w 20 -V $VIDJIL_DIR/germline/homo-sapiens/TRDV.fa -V $VIDJIL_DIR/germline/homo-sapiens/TRDD2_upstream.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDD3_downstream.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDJ.fa $VIDJIL_D
ATA
/trd-dd2-dd3.fa
$ Segment all 8 reads, thanks to TRDD2 and TRDD3
1: junction detected in 8 reads .100..
...
...
algo/tests/should-get-tests/unsegmentation-causes-u.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -u $VIDJIL_D
IR/data
/segmentation-2.fa ; cat ./out///segmentation-2.UNSEG_ambiguous.fa ; cat ./out///segmentation-2.UNSEG_too_few_V_J.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -u $VIDJIL_D
ATA
/segmentation-2.fa ; cat ./out///segmentation-2.UNSEG_ambiguous.fa ; cat ./out///segmentation-2.UNSEG_too_few_V_J.fa
$ The proper unsegmentation cause is given
1: UNSEG too short -> .* 1
...
...
algo/tests/should-get-tests/unsegmentation-causes.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -uuu $VIDJIL_D
IR/data
/segmentation-2.fa ; cat out/segmentation-2.unsegmented.vdj.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -uuu $VIDJIL_D
ATA
/segmentation-2.fa ; cat out/segmentation-2.unsegmented.vdj.fa
$ Only one sequence is segmented, but it is too small for a window (too short w)
1: junction detected in 1 reads
...
...
algo/tests/should-get-tests/vidjil-error-w-small.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 1 -w -10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/Stanford_S22.fasta 2>&1
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 1 -w -10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/Stanford_S22.fasta 2>&1
!EXIT_CODE: 1
$ Error, too small -w
...
...
algo/tests/should-get-tests/vidjil-small-w.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 100 -r 1 -y 1 -z 0 -w 10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/Stanford_S22.fasta 2>&1
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 100 -r 1 -y 1 -z 0 -w 10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/Stanford_S22.fasta 2>&1
!OUTPUT_FILE: out/seq/clone.fa-1
### !EXIT_CODE: 1
...
...
algo/tests/should-get-tests/vidjil-warning-A.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/toy_V.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/toy_V.fa
$ Warning, -A
1:WARNING
...
...
algo/tests/should-get-tests/vidjil-warning-z.should-get
View file @
880abf7d
!NO_LAUNCHER:
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 200 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/trd-dd2-dd3.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 200 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/trd-dd2-dd3.fa
$ Warning, -z
1:WARNING
...
...
algo/tests/should-get-tests/vidjil_long_segment.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/long-segmentation.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/long-segmentation.fa
$ Sequence should be segmented by k-mer segmenter
e1:SEG_+ -> 1
algo/tests/should-get-tests/vidjil_revcomp_VdJa.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/ -r 1 -c clones $VIDJIL_D
IR/data
/revcomp-VdJa.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/ -r 1 -c clones $VIDJIL_D
ATA
/revcomp-VdJa.fa
$ Just one window found
1:==> found 1 ..-windows
...
...
algo/tests/should-get-tests/vidjil_revcomp_s22.should-get
View file @
880abf7d
!LAUNCH: $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_D
IR/data/Stanford_S22.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22.log && $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DIR/data
/Stanford_S22.rc.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22_rc.log && diff out/Stanford_S22{,.rc}.vidjil | grep GGG && diff vidjil_s22.log vidjil_s22_rc.log
!LAUNCH: $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_D
ATA/Stanford_S22.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22.log && $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA
/Stanford_S22.rc.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22_rc.log && diff out/Stanford_S22{,.rc}.vidjil | grep GGG && diff vidjil_s22.log vidjil_s22_rc.log
!EXIT_CODE: 1
$ Same number segmented
...
...
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